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CLOCK protein acts as a positive regulator for transcription of N-methylpurine DNA glycosylase gene.Although Clock gene product, a component of the circadian pacemaker, has been suggested to participate in the regulation of cellular sensitivity to genotoxic stress, the underlying mechanism remains to be fully understood. In this study, we showed that Clock gene mutation modulates the sensitivity of hepatocytes to alkylating agent-induced genotoxic stress through altering the expression of N-methylpurine DNA glycosylase (MPG), the first enzyme in the base excision repair pathway. Neither wild-type nor Clock mutant (Clock/Clock) mice showed a significant 24-h variation in the hepatic expression of MPG. However, the mRNA and protein levels of MPG in the liver of Clock/Clock mice were significantly lower than those in wild-type liver. The cytotoxic effect of methyl methanesulfonate (MMS), a methylating agent, on primary cultured hepatocytes prepared from Clock/Clock mice was more potent than on wild-type hepatocytes, while overexpression of MPG in Clock/Clock hepatocytes restored their MMS sensitivity to the wild-type level. These findings suggest that the product of the Clock gene controls the sensitivity of cells to genotoxic stress through regulating the expression of the MPG gene. Our present findings would provide a molecular link between the circadian clock and DNA repair pathway.